Marín-Garzón Natalia A, Mota Lucio F M, Vargas Giovana, Arikawa Leonardo M, Fonseca Larissa F S, Fernandes Júnior Gerardo A, Carvalheiro Roberto, Albuquerque Lucia G
School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Via de Acesso Prof. Paulo Donato Castelane, Jaboticabal, 14884-900, SP, Brazil.
CSIRO Agriculture and Food, Hobart, TAS, 7000, Australia.
Sci Rep. 2025 Aug 19;15(1):30364. doi: 10.1038/s41598-025-14139-0.
Ongoing advances in genome sequencing technologies have enabled the identification of numerous structural variants (SVs) in livestock genomes, which are the main determinants of complex traits due to their impact on gene expression. Thus, this study aimed to detect structural variants using whole genome re-sequencing (WGS) data and identify positional candidate genes and quantitative trait loci (QTL) overlapping the most frequent SV regions in Nellore cattle. The WGS from 151 representative Nellore bulls were analyzed to conduct genome-wide structural variation calling and to identify common SV regions. Gene and QTL information surrounding the most frequent SV regions was identified using the Ensembl Genes and Cattle QTL database. The identified genes were functionally classified for biological mechanisms and pathways (Gene Ontology - GO) using the panther database. A total of 215,031 SVs were identified, with most of them being copy number variants (CNV) (183,032 deletions and 14,013 duplications) and 17,986 inversions (INV). These SVs cover, on average, 4.81% of the autosomal genome. Furthermore, we found 3,752 non-redundant SV regions that are frequent in at least 5% of the bulls. These SV regions mainly correspond to CNV regions (97%) and inversion regions (3%). In total, all SV regions cover 13.13% of the total autosomal genome, with 11.4% attributed to CNV regions and 1.7% to inversion regions. Moreover, we found that 532 SV regions were common in more than 50% of the bulls evaluated and overlapped 130 QTL previously associated with economically important traits related to exterior, health, meat and carcass, milk, production, and reproduction. A total of 1,164 positional candidate genes were identified, with 204 SVRs overlapping these genes. These genes are significantly overrepresented in GO terms related to biological processes (BP), molecular functions (MF), and biochemical pathways, playing an essential role in environmental adaptation mechanisms and feed efficiency indicator traits. Our results suggest that genes surrounding SV regions play key biological functions essential to thermotolerance, immunity, metabolism, tissue integrity, and environmental adaptation in tropical regions.
基因组测序技术的不断进步使得家畜基因组中众多结构变异（SVs）得以鉴定，这些结构变异因其对基因表达的影响，是复杂性状的主要决定因素。因此，本研究旨在利用全基因组重测序（WGS）数据检测结构变异，并鉴定与内洛尔牛中最常见SV区域重叠的位置候选基因和数量性状基因座（QTL）。对151头代表性内洛尔公牛的WGS进行分析，以进行全基因组结构变异检测并识别常见的SV区域。利用Ensembl基因和牛QTL数据库识别最常见SV区域周围的基因和QTL信息。使用泛素数据库对鉴定出的基因进行生物学机制和途径（基因本体论 - GO）的功能分类。共鉴定出215,031个SV，其中大多数是拷贝数变异（CNV）（183,032个缺失和14,013个重复）以及17,986个倒位（INV）。这些SV平均覆盖常染色体基因组的4.81%。此外，我们发现了3,752个非冗余SV区域，这些区域在至少5%的公牛中频繁出现。这些SV区域主要对应于CNV区域（97%）和倒位区域（3%）。总体而言，所有SV区域覆盖常染色体基因组总数的13.13%，其中11.4%归因于CNV区域，1.7%归因于倒位区域。此外，我们发现532个SV区域在超过50%的评估公牛中常见，并且与先前与外观、健康、肉和胴体、牛奶、生产和繁殖等经济重要性状相关的130个QTL重叠。共鉴定出1,164个位置候选基因，其中204个SVR与这些基因重叠。这些基因在与生物过程（BP）、分子功能（MF）和生化途径相关的GO术语中显著富集，在环境适应机制和饲料效率指标性状中发挥重要作用。我们的结果表明，SV区域周围的基因在热带地区的耐热性、免疫力、新陈代谢、组织完整性和环境适应中发挥着关键的生物学功能。
